On the selection and design of proteins and peptide derivatives for the production of photoluminescent, red-emitting gold quantum clusters

Novel pathways of the synthesis of photoluminescent gold quantum clusters (AuQCs) using biomolecules as reactants provide biocompatible products for biological imaging techniques. In order to rationalize the rules for the preparation of red-emitting AuQCs in aqueous phase using proteins or peptides, the role of different organic structural units was investigated. Three systems were studied: proteins, peptides, and amino acid mixtures, respectively. We have found that cysteine and tyrosine are indispensable residues. The SH/S-S ratio in a single molecule is not a critical factor in the synthesis, but on the other hand, the stoichiometry of cysteine residues and the gold precursor is crucial. These observations indicate the importance of proper chemical behavior of all species in a wide size range extending from the atomic distances (in the AuI-S semi ring) to nanometer distances covering the larger sizes of proteins assuring the hierarchical structure of the whole self-assembled system

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs

Crystallisation route map

A route map for the assessment of crystallisation processes is presented. A theoretical background on solubility, meta-stable zone width, nucleation and crystal growth kinetics is presented with practical examples. The concepts of crystallisation hydrodynamics and the application of population balances and computational fluid dynamics for modelling crystallisation processes and their scaling up are also covered

Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

The crystallographic structures of the α- and β- polymorphic forms of para aminobenzoic acid are deconstructed into their constituent hydrogen bonding molecular structural building blocks of monomers, dimers, tetramers and octamers, where they are analysed using ab initio quantum mechanical calculations of their conformation and cluster stability in solution. The molecular conformation found in the β-form is less stable than the same found in the α-form for both the gas and solution phases, suggesting that this causes a slight increase in the barrier to the crystallisation of the β-form in comparison to the α-form. The solution populations of the self-associated OH⋯O H-bonding ‘classic carboxylic acid dimer’, present in the α- and not the β-structure, is calculated to dominate in acetonitrile, dimethyl sulfoxide, ethanol, ethyl acetate, methanol, nitromethane and water. It is observed that this classic dimer is least stable in water, compared to the other PABA crystallisation solvents, with the OH⋯N H-bonding interaction present in the β-form being the second most stable dimeric interaction. These results are discussed in terms of the crystallisability and polymorphic behaviour of the α and β forms of PABA from the afore mentioned crystallisation solvents, whilst detailing how this approach could be reproducible for a range of polymorphic crystalline materials

Desorption of rare earth elements (REEs) from schwertmannite under acid mine drainage (AMD) and AMD-seawater conditions

Schwertmannite as a sink for rare earth elements (REEs) in environments affected by acid mine drainage (AMD) plays a significant role in the fate of these elements. The conditions to precipitate schwertmannite (i.e., sulfate-rich water and pH between 2.5 and 3.5) are not suitable for this Fe-oxyhydroxysulfate (Fe8O8(OH)6SO4) to adsorb REEs. In estuaries where AMD-impacted rivers meet (e.g. the Odiel and the Tinto rivers in the Ría de Huelva estuary in SW Spain), AMD mixes with seawater raising the pH between 4.5 and 8, thereby enabling REE adsorption on schwertmannite at circumneutral pH. However, the estuarine tidal dynamics exposes REE-enriched schwertmannite to more acidic water, inducing REE desorption, which has yet to be studied. In the present work, batch experiments were performed to study the REE desorption from a REE-enriched schwertmannite within the pH range 4.5–7 in the presence of sulfate at room temperature. Solution-chemistry data were used to obtain the REE desorption surface constants from different surface complexation. Desorption of a Lu-enriched schwertmannite at different pH was investigated with High Energy X-Ray Diffraction (HEXD) and Extended X-ray Adsorption Fine Structure (EXAFS) to characterize the changes in the surface complexes during desorption. The results indicate that (1) REEs desorb from schwertmannite at pH < 6 and desorption is pH dependent, (2) desorption of light REEs is higher than that of heavy REEs, (3) REE sorption onto schwertmannite surface is not a totally reversible reaction, and that (4) both monodentate and bidentate surface complexes are involved in the Lu-desorption reaction. These observations indicate that (1) REE-enriched schwertmannite remains stable in the areas of the estuary nearer the sea and that (2) tidal fluctuations displace schwertmannite colloids towards areas that are more affected by AMD, inducing REE desorption from schwertmannite

The impact of stoichiometry on the initial steps of crystal formation: Stability and lifetime of charged triple-ion complexes

Minerals form in natural systems from solutions with varying ratios of their lattice ions, yet non-stoichiometric conditions have generally been overlooked in investigations of new formation (nucleation) of ionic crystals. Here, we investigated the influence of cation:anion ratio in the solution on the initial steps of nucleation by studying positively and negatively charged triple ion complexes and subsequent particle size evolution. Our model systems are carbonates and sulfates of calcium and barium, as it was recently shown that solution stoichiometry affects the timing and rate of their nucleation. Molecular dynamics (MD) simulations and dynamic light scattering (DLS) flow experiments show that nucleation correlates with the stability and lifetime of the initial complexes, which were significantly impacted by the cation:anion stoichiometry and ion type. Specifically, (Formula presented.) was found to have higher association constants and its lifetime was twofold longer than (Formula presented.). Similar trends were observed for (Formula presented.) and (Formula presented.). Contrastingly, for (Formula presented.), (Formula presented.) was found to have lower association constants and its lifetime was shorter than (Formula presented.). These trends in stability and lifetime follow the same asymmetrical behaviour as observed experimentally for particle formation using techniques like DLS. This suggests a causal relationship between the stability and lifetime of the initial charged complexes and the nucleation under non-stoichiometric conditions

The thermal expansion coefficients of the alpha and beta polymorphic forms of p-aminobenzoic acid in relation to their bulk crystal chemistry

The thermal expansion behaviour of the alpha and beta polymorphs of para-aminobenzoic acid are presented and discussed in terms of the bulk crystal chemistry and the associated strengths of the constituent intermolecular synthons for these two materials. Analysis of temperature dependant powder diffraction data over the temperature range 298.15–403.15 K facilitates calculation of the linear thermal expansion coefficients: αa = 8.36 × 10−06 K−1, αb = 94.5 × 10−06 K−1 and αc = 9.91 × 10−06 K−1 for the alpha polymorph and αa = 21.5 × 10−06 K−1, αb = 48.5 × 10−06 K−1 and αc = 2.22 × 10−06 K−1 for the beta polymorph. The exceptionally large increase in the thermal expansion of the b axis for the alpha form reflects the weak dispersive interactions which propagate along this axis. In contrast, the a and c axes contain relatively strong hydrogen bonds which stabilise the lattice and limit thermal expansion. The thermal expansion of the beta form reflects the more isotropic nature of the intermolecular synthons for this polymorph in comparison to the alpha form. The thermal expansion of the b axis of the beta form is larger than that of the a and c axes but to a much lesser extent than that observed for the alpha form. This is rationalised through identification of a hydrogen bonding component which contributes to the stabilisation of the b axis in comparison to the almost fully dispersive nature found in the alpha structure

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed

Revealing the Roles of Desolvation and Molecular Self-Assembly in Crystal Nucleation from Solution: Benzoic and p -Aminobenzoic Acids

There has been much recent interest in the role of solution chemistry and in particular the importance of molecular self-assembly in the nucleation of crystalline phases. Techniques such as FTIR and NMR have highlighted the existence of solution-phase dimers which in many cases mirror the structural synthons found in the resulting macroscopic crystals. However, there are no reported examples in which this new insight into the solution phase has been linked directly to the kinetics of crystal nucleation. Here for the first time, using a combination of solution FTIR, computational chemistry, and measured crystal nucleation rate data, such a link is demonstrated for p-aminobenzoic (PABA) and benzoic acids nucleating from polar and nonpolar solvents. Solute dimerization and desolvation are found to be rate-determining processes in the overall nucleation pathway

Towards an understanding of the nucleation of alpha-para amino benzoic acid from ethanolic solutions: A multi-scale approach

The molecular assembly and subsequent nucleation of para-amino benzoic acid (PABA) from ethanolic solutions is probed using a multi-scale and multi-technique approach. This is applied by examining and interrelating information regarding the molecular, solution-state, cluster, solid-state and surface structures to understand why the alpha form of PABA is crystallised in preference to its low temperature beta form. Calculations suggest that conformational changes within the solute molecule play little or no role in directing the nucleation of either the alpha or beta crystal forms. Combined ab initio and molecular dynamics calculations of the stability of small clusters in solution suggests that the hydrogen-bonded carboxylic acid dimers, present in the alpha structure, are the most stable in solution and play a major role in the self-assembly and polymorphic expression of the alpha form in ethanol in preference to the beta form. These calculations are in good agreement with X-ray small-angle scattering analysis which reveals the presence of PABA clusters in ethanol which are consistent with the size and shape of a carboxylic acid dimer. SAXS studies also reveal the presence of larger cluster structures in a size range 10-40 nm which appear to grow, perhaps reflecting a change in the balance between monomers and dimers within the solution during the nucleation process. The results of crystallisation-kinetics experiments indicate an instantaneous nucleation mechanism where the number of instantaneously nucleated crystallites is calculated to be 1360-660 nuclei per ml and the subsequent growth is found to be only rate limited by diffusion of the growth unit to the crystallite surface. A linear dependence of growth rate with respect to supersaturation is observed for the (0 1 -1) capping face, which is associated with strong π-π stacking interactions. This is consistent with a solid-on-solid mechanism associated with surface roughened growth and concomitant poor lattice-perfection. Conversely, the side (1 0 -1) surface has a growth mechanism consistent with a 2D nucleation birth and spread mechanism. Hence, these mechanisms result in very fast growth along the b-axis and the needle-like morphology that is observed for alpha-PABA